Safety alignment of large reasoning models (LRMs) via supervised fine-tuning (SFT) and reinforcement learning (RL) often yields near-perfect safety scores, yet this apparent success comes at the cost of severe over-refusal and degraded general capabilities. Through systematic empirical analysis, we find that these failures are closely associated with the learning of spurious shortcuts rather than robust intent-sensitive safety evaluation. Specifically, we identify two dominant shortcuts: formatting shortcuts, where refusal behaviors are overly bound to structural prompt templates that frequently appear in safety alignment corpora; and lexical shortcuts, where sensitive keywords reflexively trigger refusals on benign queries. To mitigate reliance on these shortcuts, we propose DeShortcut-Align, a shortcut-decoupling alignment framework that reduces dependence on superficial cues. DeShortcut-Align operates across three coordinated stages: (1) Refusal Sensitivity Attribution, which masks input tokens to quantify their impact on the final refusal response distribution; (2) Attribution-Guided Contrastive Augmentation, which constructs benign contrastive samples using high-sensitivity tokens to mitigate lexical shortcuts; and (3) Counterfactual Consistency Regularization, which constructs template-ablated states via attention blinding to enforce decision consistency across SFT and RL, mitigating formatting shortcut dependence. Experiments on 7B and 14B models demonstrate that DeShortcut-Align significantly improves robustness against template-stripping bypass attacks (reducing performance drops by up to 72%), substantially reduces over-refusal by over 58%, and better preserves general-purpose reasoning capabilities, thereby mitigating the alignment tax commonly observed in safety training.

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